Re: [Gusdev-gusdev] "RE-GENERATE THE GUS OBJECTS"

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Plus it should be:

SResVer::MassSpecSummaryVER

(note the Ver on the end of the table)

I think MassSpecSummary should be in DoTS, not SRES.

--Mike

On Jun 9, 2004, at 5:00 PM, Steve Fischer wrote:

> michael-
>
> it looks like you added a row to TableInfo for the  
> SResVer::MassSpecSummary.   if so, delete it and build again.
>
> steve
>
> Michael Luchtan wrote:
>
>> It has been a long time since a build took place here, and I was not
>> really present for the installation of GUS.  But in the checkouts
>> directory I checked out GUS from Sanger.  I executed the build GUS  
>> install -append
>> and got the following errors:
>>     [exec] generating java object for SResVer::MassSpecSummary
>>     [exec] Error:  Package Table Name '' is not in the form of
>> org.gusdb.model.SCHEMA.NAME at /var/lo\
>> cal/gus_home/lib/perl/GUS/ObjRelP/Generator/RowGenerator.pm line 91
>>     [exec]     
>> GUS::ObjRelP::Generator::RowGenerator::_cutPackageTableName('GUS:: 
>> ObjRelP::Generator::\
>> JavaRowGenerator=HASH(0x83955d0)', undef) called at
>> /var/local/gus_home/lib/perl/GUS/ObjRelP/Generator\
>> /JavaRowGenerator.pm line 410
>>     [exec]     
>> GUS::ObjRelP::Generator::JavaRowGenerator:: 
>> _createParentAccessors('GUS::ObjRelP::Gener\
>> ator::JavaRowGenerator=HASH(0x83955d0)', 'HASH(0x85d48ec)') called at
>> /var/local/gus_home/lib/perl/GUS\
>> /ObjRelP/Generator/JavaRowGenerator.pm line 127
>>     [exec]     
>> GUS::ObjRelP::Generator::JavaRowGenerator::_genAccessors('GUS:: 
>> ObjRelP::Generator::Jav\
>> aRowGenerator=HASH(0x83955d0)') called at
>> /var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/JavaRowGe\
>> nerator.pm line 32
>>     [exec]     
>> GUS::ObjRelP::Generator::JavaRowGenerator::generate('GUS::ObjRelP:: 
>> Generator::JavaRowG\
>> enerator=HASH(0x83955d0)', undef) called at
>> /var/local/gus_home/lib/perl/GUS/ObjRelP/Generator/Generat\
>> or.pm line 109
>>     [exec]     
>> GUS::ObjRelP::Generator::Generator::generate('GUS::ObjRelP:: 
>> Generator::Generator=HASH(\
>> 0x81073d4)', undef) called at  
>> /var/local/gus_home/bin/generateGusObjects
>> line 67
>>
>> BUILD FAILED
>> file:/var/local/checkout/GUS/build.xml:114: exec returned: -1
>>
>>
>> According to the VBI install docs, it is necessary to edit the  
>> build.xml
>> and take out the generateGusObjects executable statement first.  But
>> after this I get the following errors:
>>      [echo] Installing GUS/Model
>>    [javac] Compiling 5 source files to
>> /var/local/checkout/GUS/Model/classes
>>    [javac]
>> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/ 
>> MassSpecSummary_Table.java:\
>> 17: illegal start of expression
>>    [javac]         tableAtts.put("", new GUSTableAttribute("", "",
>> "java.lang.notdefyet", -1, , -1, f\
>> alse, false) );
>>   [javac]                                                              
>>                            ^
>>    [javac]
>> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/SResVer/ 
>> MassSpecSummary_Table.java:\
>> 17: ')' expected
>>    [javac]         tableAtts.put("", new GUSTableAttribute("", "",
>> "java.lang.notdefyet", -1, , -1, f\
>> alse, false) );
>>   [javac]                                                              
>>                               \
>>                  ^
>>    [javac] 2 errors
>>
>> BUILD FAILED
>> file:/var/local/checkout/install/build.xml:227: Compile failed; see  
>> the
>> compiler error output for deta\
>> ils.
>>
>>
>> Any help is appreciated....
>> Michael Luchtan
>>
>>
>>
>>
>>
>> On Wed, 2004-06-09 at 16:10, Steve Fischer wrote:
>>
>>> michael-
>>>
>>> we have seen this.  i think if you get the latest from cvs and then  
>>> rebuild the objects you will get around this problem.
>>> then, use submitrow to add rows to tableinfo for the mass spec  
>>> tables and rebuild all over again.
>>>
>>> steve
>>>
>>> Michael Luchtan wrote:
>>>
>>>
>>>> Hello--
>>>> Can you give me a heads up on why I cannot use the submitrow plugin  
>>>> any
>>>> more, now that I have rebuild the perl object layer?  Hope I didn't  
>>>> just
>>>> screw myself...
>>>>
>>>> Here is the command/arguement:
>>>>
>>>> luchtan]# ga GUS::Common::Plugin::SubmitRow --tablename  
>>>> Core::UserInfo
>>>> --attrlist
>>>> "login,password,first_name,last_name,e_mail,modification_date"
>>>> --valuelist
>>>> "pablo^^^pablo123^^^pablo^^^mendes^^^pa...@pa...^^^SYSDATE 
>>>> "
>>>> Reading properties from  
>>>> /var/local/gus_home/config/GUS-PluginMgr.prop
>>>> Reading properties from /home/luchtan/.gus.properties
>>>> DBD::Oracle::st execute failed: ORA-00001: unique constraint
>>>> (CORE.PK_ALGORITHMINVOCATION) violated (DBD ERROR: OCIStmtExecute)  
>>>> at
>>>> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
>>>>
>>>> SQL ERROR!! involving
>>>>
>>>>   INSERT INTO Core.AlgorithmInvocation (  end_time, row_user_id,
>>>> user_write, group_write, cpu_time, algorithm_implementation_id,
>>>> row_project_id, algorithm_invocation_id, comment_string, group_read,
>>>> row_group_id, result, other_read, cpus_used, start_time,
>>>> modification_date, user_read, row_alg_invocation_id, other_write,
>>>> machine_id )
>>>>   VALUES   (  SYSDATE, ?, ?, ?, ?, ?, ?, ?, '', ?, ?, ?, ?, ?,
>>>> SYSDATE, SYSDATE, ?, ?, ?, ? )
>>>> Values: 4, 1, 1, 0, 3, 2, 25, 1, 2, pending, 1, 1, 1, 1, 0, 0 at
>>>> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>>>>       
>>>> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP:: 
>>>> DbiDbHandle=HASH(0x855e940)', '^J SQL ERROR!! involving^J ^J     
>>>> INSERT INTO Core.AlgorithmInvocati...') called at  
>>>> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>>>>       
>>>> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP:: 
>>>> DbiDbHandle=HASH(0x855e940)',  
>>>> 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x873690c)',  
>>>> 'ARRAY(0x87377c4)', '^J    INSERT INTO Core.AlgorithmInvocation (   
>>>> end_time, row_user_...') called at  
>>>> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
>>>>       
>>>> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::Core:: 
>>>> AlgorithmInvocation=HASH(0x86ae1ac)', 'HASH(0x86a9574)') called at  
>>>> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621
>>>>       
>>>> GUS::ObjRelP::DbiRow::insert('GUS::Model::Core:: 
>>>> AlgorithmInvocation=HASH(0x86ae1ac)') called at  
>>>> /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>>>>       
>>>> GUS::Model::GusRow::submit('GUS::Model::Core:: 
>>>> AlgorithmInvocation=HASH(0x86ae1ac)') called at  
>>>> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
>>>> 939
>>>>       
>>>> GUS::PluginMgr::GusApplication::openInvocation('GUS::PluginMgr:: 
>>>> GusApplication=HASH(0x80fbb4c)',  
>>>> 'GUS::Common::Plugin::SubmitRow=HASH(0x850872c)') called at  
>>>> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
>>>> 425
>>>>       
>>>> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:: 
>>>> GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow')  
>>>> called at  
>>>> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
>>>> 283
>>>>       
>>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr:: 
>>>> GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::SubmitRow')  
>>>> called at  
>>>> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line  
>>>> 192
>>>>       
>>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr:: 
>>>> GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at  
>>>> /var/local/gus_home/bin/ga line 11
>>>> Issuing rollback() for database handle being DESTROY'd without  
>>>> explicit
>>>> disconnect().
>>>>
>>>>
>>>> On Wed, 2004-06-09 at 14:52, Steve Fischer wrote:
>>>>
>>>>
>>>>> I have added instructions for this to the wiki.   see if you can  
>>>>> find it.
>>>>>
>>>>> steve
>>>>>
>>>>> Michael Luchtan wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hello-
>>>>>> We are attempting to load some mass spec data into gus.  Well, the
>>>>>> version of gus that we have did not contain two of the relevant  
>>>>>> tables:
>>>>>> DoTS.MassSpecFeature and DoTS.MassSpecSummary
>>>>>> I created the MassSpecFeature view on DoTS.aafeatureimp and the  
>>>>>> table
>>>>>> dots.massspecsummary. Now we need to generate the GUS objects for  
>>>>>> the tables for use in
>>>>>> plug-ins.  All of the oerl modules in GUS/Model/* are generated
>>>>>> automagically.  It looks like I could just copy some files and  
>>>>>> change
>>>>>> the names.  But they all say something like this:
>>>>>>
>>>>>> # THIS CLASS HAS BEEN AUTOMATICALLY GENERATED BY THE
>>>>>> GUS::ObjRelP::Generator
>>>>>> # PACKAGE.
>>>>>> #
>>>>>> # DO NOT EDIT!!
>>>>>>
>>>>>> # TO ADD FUNCTIONALITY MANUALLY, COPY THIS FILE TO
>>>>>> InteractionType.pm.man
>>>>>> # (or edit that file if it already exists) AND ADD THE  
>>>>>> FUNCTIONALITY
>>>>>> THERE.
>>>>>> # THEN RE-GENERATE THE GUS OBJECTS.
>>>>>>
>>>>>> Any word on how to use the Generator?  Any help is appreciated.   
>>>>>> It
>>>>>> might go well in the Wiki-wiki!
>>>>>>
>>>>>> Michael Luchtan
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> -------------------------------------------------------
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>>>>>
>>>>>
>>>>
>>>> -------------------------------------------------------
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>>>> Hackers Unite!  GUADEC: The world's #1 Open Source Desktop Event.
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>>>> Norway
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>>>>
>>>>
>
>
>
> -------------------------------------------------------
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> http://2004/guadec.org
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